On the use of the coefficient of variation to quantify and compare trait variation

ColorNet: An AI-based framework for pork freshness detection using a colorimetric sensor array

Pork freshness is crucial for flavour, nutrition and consumer health. The current colorimetric sensor array (CSA) detection systems face challenges related to high sensor development costs, low recognition accuracy and limitations in the platform use. Herein, we developed a CSA and ColorNet framework to detect pork freshness. The 53-point CSA was designed by selecting sensitised pH indicators and aldehyde/ketone indicators. To optimize the sensor, the Euclidean distance method was used to identify 24 array points with dyes that exhibited more sensitive responses. The ColorNet captured the color information of pork freshness, allowing real-time detection with a 99.5 % accuracy. For practical deployment and mobile applications, a refined 12-point CSA was developed using gradient activation mapping, maintaining a 99 % recognition rate, which is comparable with the 24-point CSA. The proposed CSA and model ensure consumer health and safety, providing strong technical support for quality monitoring and control in the pork industry.

Synergistic interplay of management practices and environmental factors in shaping grassland soil carbon stocks: Insights into the effects of fertilization, mowing, burning, and grazing

Grasslands, which account for over 40 % of the Earth's terrestrial area, play a vital role in mitigating global change and biodiversity loss. These ecosystems serve as critical carbon sinks, regulating the global carbon cycle and supporting diverse flora and fauna. However, their ability to sustain these functions is threatened by land use change and climate disruption. Current challenges revolve around understanding how key management practices such as grazing, mowing, burning, and fertilization, interact with environmental factors to influence grassland soil carbon stocks. This study presents a meta-analysis of the effects of these management practices and environmental factors, such as soil type, depth, texture, temperature, precipitation, and their synergistic interplay. It evaluates how management intensity, duration, and frequency interact with these environmental variables to influence soil carbon storage, providing valuable insights into optimizing grassland management for enhanced soil carbon stock and broader ecosystem stability. The findings reveal that grazing, particularly at high intensity, tends to reduce soil carbon stocks (-0.412, p < 0.001), with the most pronounced effects observed in shallow soils and temperate climates. Mowing also negatively affected carbon stock (-0.416, p = 0.013), especially when carried out frequently and over long durations. On the other hand, burning had mixed results with an overall positive effect (0.340, p = 0.078). Short-term burns promoted carbon accumulation, while frequent burning led to carbon loss. Fertilization, especially with nitrogen and phosphorus, proved beneficial for increasing soil carbon stocks (0.712, p < 0.001), particularly in nutrient-poor soils and semi-arid climates. This study introduces a systems-based approach to grassland management, providing a framework for optimizing carbon-focused strategies. By integrating the role of management practices, particularly their frequency, intensity, and duration, along with soil characteristics and climate, these findings provide actionable insights for policymakers, land managers, and researchers. They guide the development of sustainable management strategies that not only enhance soil carbon stocks but also support ecosystem health and resilience.

Frontal sinus size in South African Later Stone Age Holocene Khoe-San

Frontal size variation is comparatively poorly sampled among sub-Saharan African populations. This study assessed frontal sinus size in a sample of Khoe-San skeletal remains from South African Later Stone Age contexts. Volumes were determined from CT scans of 102 adult crania; individual sex could be estimated in 82 cases. Sinus volume is not sexually dimorphic in this sample. The lack of frontal sinus aplasia is concordant with the low incidences recorded for other sub-Saharan African and most other global populations save those that inhabit high latitudes. There is considerable variation in frontal sinus size among global populations, and the Khoe-San possess among the smallest. The Khoe-San have rather diminutive sinuses compared to sub-Saharan Bantu-speaking populations but resemble a northern African (Sudanese) population. Genetic studies indicate the earliest population divergence within Homo sapiens to have been between the Khoe-San and all other living groups, and that this likely occurred in Africa during the span of Marine Isotope Stages 8-6. There is scant information on frontal sinus development among Late Quaternary African fossils that are likely either closely related or attributable to Homo sapiens. Among these, the MIS 3 cranium from Hofmeyr, South Africa, exhibits distinct Khoe-San cranial affinities and despite its large size has a very small frontal sinus. This raises the possibility that the small frontal sinuses of the Holocene South African Khoe-San might be a feature retained from an earlier MIS 3 population.

Longitudinal Evaluation of the Risk Index for Overdose or Serious Opioid-Induced Respiratory Depression in Patients with Cancer

The Commercially Insured health Plan Risk Index for Overdose or Serious Opioid-induced Respiratory Depression (CIP-RIOSORD) is an evidence-based screening tool to determine an individual's risk of opioid-induced respiratory depression (OIRD) or overdose. Chronic opioid use and changes in a patient's clinical status and/or medication regimen may impact OIRD or overdose risk. This study evaluated longitudinal CIP-RIOSORD scores over three consecutive visits. Data for eighty patients with cancer encompassed two-hundred and forty visits. Most patients were Caucasian women with metastatic gastrointestinal cancer. CIP-RIOSORD scores (mean ± SD) were 16.6 ± 15.4, 20.3 ± 15.7, and 19.1 ± 15.1 at visits 1, 2, and 3, respectively. Visit 1 CIP-RIOSORD scores were similar compared to visit 2 and visit 3 (p = 0.14-0.31). CIP-RIOSORD intraindividual variability was low to moderate; the median (range) coefficient of variation was 22.3% (0-173%). Beyond a baseline OIRD/overdose risk assessment, reevaluation of such risk using the CIP-RIOSORD does not to be performed at each palliative care visit.

Floral phenotypic divergence and genomic insights in an Ophrys orchid: unraveling early speciation processes

Adaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape. Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: variation and integration of floral components (scent, color and shape); phenotypes and genomic regions under divergent selection; and the genomic bases of trait variation. We identified a large genomic island of divergence, likely associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while stabilizing selection was suspected on floral morphology and for several volatile olfactive compounds. We also identified candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor. This study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, that is the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes.

Quantifying Genetic Parameters for Blackleg Resistance in Rapeseed: A Comparative Study

Selection is a fundamental part of the plant breeding process, enabling the identification and development of varieties with desirable traits. Thanks to advances in genetics and biotechnology, the selection process has become more precise and efficient, resulting in faster breeding progress and better adaptation of crops to environmental challenges. Genetic parameters related to gene additivity and epistasis play a key role and can influence decisions on the suitability of breeding material. In this study, 188 rapeseed doubled haploid lines were assessed in field conditions for resistance to Leptosphaeria spp. Through next-generation sequencing, a total of 133,764 molecular markers (96,121 SilicoDArT and 37,643 SNP) were obtained. The similarity of the DH lines at the phenotypic and genetic levels was calculated. The results indicate that the similarity at the phenotypic level was markedly different from the similarity at the genetic level. Genetic parameters related to additive gene action effects and epistasis (double and triple) were calculated using two methods: based on phenotypic observations only and using molecular marker observations. All evaluated genetic parameters (additive, additive-additive and additive-additive-additive) were statistically significant for both estimation methods. The parameters associated with the interaction (double and triple) had opposite signs depending on the estimation method.

Fundamental equations linking methylation dynamics to maximum lifespan in mammals

We describe a framework that addresses concern that the rate of change in any aging biomarker displays a trivial inverse relation with maximum lifespan. We apply this framework to methylation data from the Mammalian Methylation Consortium. We study the relationship of lifespan with the average rate of change in methylation (AROCM) from two datasets: one with 90 dog breeds and the other with 125 mammalian species. After examining 54 chromatin states, we conclude three key findings: First, a reciprocal relationship exists between the AROCM in bivalent promoter regions and maximum mammalian lifespan: AROCM ∝ 1/MaxLifespan. Second, the correlation between average methylation and age bears no relation to maximum lifespan, Cor(Methyl,Age) ⊥ MaxLifespan. Third, the rate of methylation change in young animals is related to that in old animals: Young animals' AROCM ∝ Old AROCM. These findings critically hinge on the chromatin context, as different results emerge in other chromatin contexts.

Short-term fluctuating and long-term divergent selection on sympatric Monkeyflowers: insights from decade-spanning reciprocal transplants

Sympatric species are often locally adapted to distinct microhabitats. However, temporal variation may cause local maladaptation and species boundary breakdown, especially during extreme climatic events leading to episodic selection. Repeated reciprocal transplants can reveal the interplay between short and long-term patterns of natural selection. To examine evolutionary trajectories of sympatric Monkeyflowers adapted to different niches, Mimulus guttatus and M. laciniatus, we performed three replicated transplants and combined them with previous experiments to leverage a dataset of five transplants spanning 10 years. We performed phenotypic selection analyses on parents and hybrids in parental habitats in Yosemite NP, CA during years of drastically differing snowpack. If there is ecological isolation, then we predicted divergent phenotypic selection between habitats in line with species' differences and local adaptation. We found interannual fluctuations in phenotypic selection, often in unpredicted directions. However, a combined-year analysis detected longer-term divergent selection on flowering time, a key temporally isolating and adaptative trait, suggesting that selection may reinforce species boundaries despite short-term fluctuations. Finally, we found temporal variation in local adaptation with M. laciniatus locally adapted in low snowpack years, while an extremely high snowpack year contributed to average local maladaptation of M. guttatus.

On the importance of scale in evolutionary quantitative genetics

The informed use of scales and units in evolutionary quantitative genetics is often neglected, and naïve standardizations can cause misinterpretations of empirical results. A potentially influential example of such neglect can be found in the recent book by Arnold (2023. Evolutionary quantitative genetics. Oxford University Press). There, Arnold championed the use of heritability over mean-scaled genetic variance as a measure of evolutionary potential arguing that mean-scaled genetic variances are correlated with trait means while heritabilities are not. Here, we show that Arnold's empirical result is an artifact of ignoring the units in which traits are measured. More importantly, Arnold's argument mistakenly assumes that the goal of mean scaling is to remove the relationship between mean and variance. In our view, the purpose of mean scaling is to put traits with different units on a common scale that makes evolutionary changes, or their potential, readily interpretable and comparable in terms of proportions of the mean.

Using PRECIS-2 in Chinese herbal medicine randomized controlled trials for irritable bowel syndrome: A methodological exploration based on literature

Background

The pragmatism levels of randomized controlled trials (RCTs) mean how similar the interventions delivered in the trial setting match those in the setting where the results will be applied. We aimed to investigate the association between the consistency of pragmatism among the characteristics of RCT design and its effect size of results in Chinese herbal medicine (CHM) for irritable bowel syndrome (IBS).

Methods

Eight English and Chinese language databases were searched for RCTs on CHM for IBS. Six reviewers independently assessed the pragmatism of trials using the pragmatic-explanatory continuum indicator summary 2 (PRECIS-2) tool. The consistency of pragmatism levels among the characteristics of RCT design was calculated using the coefficient of variation. Linear regression models were adopted to explore influence factors of the pragmatism of RCTs.

Results

78 RCTs were included. The level of consistency in the pragmatism for RCT's design was significantly correlated with the effect size of the results (binary outcome, r = -0.413; P = 0.005; continuous outcome, r = -0.779, P < 0.001). PRECIS-2 score was higher in trials with individualized interventions than fixed interventions (3.29 [0.32] vs 2.90 [0.32]; Cohen's d relative effect size, 0.52; P < 0.001) and in standard or usual-treatment-controlled trials than placebo-controlled (3.05 [0.37] vs 2.83 [0.28]; Cohen's d relative effect size, 0.32; P = 0.048).

Conclusion

The consistency of pragmatism level across the 9 domains of the PRECIS-2 tool in CHM IBS RCTs was positively correlated with the effect size of the results.

Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield and quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, and epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, and H3K27me3 collectively regulate SSP and starch genes with varying impact. Population transcriptome and phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing grain yield and quality in a core collection of wheat accessions. Integration of time-serial RNA-seq and ATAC-seq enables the construction of a hierarchical transcriptional regulatory network governing starch and SSP biosynthesis, identifying 42 high-confidence novel candidates. These candidates exhibit overlap with genetic regions associated with grain size and quality traits, and their functional significance is validated through expression-phenotype association analysis among wheat accessions and loss-of-function mutants. Functional analysis of wheat abscisic acid insensitive 3-A1 (TaABI3-A1) with genome editing knock-out lines demonstrates its role in promoting SSP accumulation while repressing starch biosynthesis through transcriptional regulation. Excellent TaABI3-A1Hap1 with enhanced grain weight is selected during the breeding process in China, linked to altered expression levels. This study unveils key regulators, advancing understanding of SSP and starch biosynthesis regulation and contributing to breeding enhancement.

Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice

The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages.

Low evolutionary potential for blue-green egg colouration in a wild bird population

Exploring the evolutionary architecture of female sexual traits and their potential evolvability is important to understand their possible role as postmating sexual signals. Egg colouration has been proposed to be one of these postmating sexual signals, honestly advertising female quality in birds, especially in blue-green laying species. In this study, we used an animal model in a Bayesian framework to estimate the evolvability of multiple descriptors of blue-green egg colouration and egg size in a wild long-term monitored population of spotless starlings (Sturnus unicolor). Our results show low to moderate heritability (h2 = 0.31-0.44) for 3 egg colour descriptors (blue-green chroma, chroma, and lightness) and egg size. Using the coefficient of additive genetic variance (CVA) and the evolvability (IA) as proxies of evolutionary potential of all components of this trait, we found low values of CVA for all these variables, suggesting a small evolutionary potential of these phenotypic traits, contrasting to previous results reported in another blue-green egg laying species. Our results indicate a modest raw genetic material of this trait on which sexual selection can act upon and, therefore, a small probability for these traits to respond easily to selection.

Metopism in adult South Africans and its relationship to frontal sinus size

This study documents the incidences of complete and partial metopism and their possible relationship to frontal sinus volume (FSV) in a sample of modern adult black South Africans with a view to evaluating the hypothesis that metopism affects frontal sinus hypoplasia. FSV was measured from CT scans and the incidence of metopism was recorded from direct observations of dried cadaveric crania. The sex of each individual was known. Four linear cranial dimensions were used to compute a geometric mean by which to scale FSV. The incidence of partial metopism (38%) is comparable to that reported for other population samples, although there is considerable variation among these global sample frequencies. It is significantly more common in male than female South Africans. FSV in individuals with complete metopism is smaller than average but not inordinately so. On the other hand, FSV is significantly larger in individuals with partial metopism than in those that do not present with this sutural remnant. The data on FSV in individuals with and without partial metopism contradict the hypothesis that there is a relationship between partial metopism and frontal sinus hypoplasia. As such, the metopic remnant evinced by the Late Pleistocene cranium from Hofmeyr, South Africa is unlikely to be related to its very small FSV.

Assessment of soil fertility and nutrient management strategies in calcareous soils of Khuzestan province: a case study using the Nutrient Index Value method

Soil fertility (SF) is a crucial factor that directly impacts the performance and quality of crop production. To investigate the SF status in agricultural lands of winter wheat in Khuzestan province, 811 samples were collected from the soil surface (0-25 cm). Eleven soil properties, i.e., electrical conductivity (EC), soil organic carbon (SOC), total nitrogen (TN), calcium carbonate equivalent (CCE), available phosphorus (Pav), exchangeable potassium (Kex), iron (Fe), copper (Cu), zinc (Zn), manganese (Mn), and soil pH, were measured in the samples. The Nutrient Index Value (NIV) was calculated based on wheat nutritional requirements. The results indicated that 100%, 93%, and 74% of the study areas for CCE, pH, and EC fell into the low, moderate, and moderate to high NIV classes, respectively. Also, 25% of the area is classified as low fertility (NIV < 1.67), 75% falls under medium fertility (1.67 < NIV value < 2.33), and none in high fertility (NIV value > 2.33). Assessment of the mean wheat yield (AWY) and its comparison with NIV showed that the highest yield was in the Ramhormoz region (5200 kg.ha-1), while the lowest yield was in the Hendijan region (3000 kg.ha-1) with the lowest EC rate in the study area. Elevated levels of salinity and CCE in soils had the most negative impact on irrigated WY, while Pav, TN, and Mn availability showed significant effects on crop production. Therefore, implementing SF management practices is essential for both quantitative and qualitative improvement in irrigated wheat production in Khuzestan province.

Variation, sexual dimorphism, and enlargement of the frontal sinus with age in adult South Africans

OBJECTIVES

To document frontal sinus volume (FSV) in a sample of sub-Saharan Africans with a view to evaluating claims that such populations exhibit comparatively small sinuses. This study also addresses questions related to sexual dimorphism, incidence of sinus aplasia, and the possibility that FSV continues to increase through adulthood.

MATERIALS AND METHODS

FSV was measured from CT scans of adult crania from the Dart Collection. Sex and age were known for each individual. Linear cranial dimensions were used to compute a geometric mean from which a scaled FSV was computed for each cranium.

RESULTS

FSV does not differ significantly between sexes, but females exhibit a higher incidence of aplasia. There is considerable variation in FSV in this sample, with the average ranking among the higher means reported for other population samples. The incidence of FS aplasia falls within the range of values recorded for other population samples. Although our study is cross-sectional rather than longitudinal, there is strong evidence that FSV continues to increase with age throughout adulthood.

DISCUSSION

The FSV mean of our sample contradicts the notion that sub-Saharan Africans possess small sinuses. In a global context, geography (climate and altitude) does not appear to be related to FSV. The absence of sexual dimorphism in our sample is unexpected, as significant dimorphism has been reported for most other population samples. Our results support other indications that the frontal sinus continues to expand throughout adulthood, especially in females, and that it is likely due to bone resorption.

Estimating Transcriptome Diversity and Specialization in Capsicum annuum L

Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means.

A novel approach to evaluation of tumor response for advanced pulmonary adenocarcinoma using the intertumoral heterogeneity response score

Treatment response and prognosis estimation in advanced pulmonary adenocarcinoma are challenged by the significant heterogeneity of the disease. The current Response Evaluation Criteria in Solid Tumors (RECIST) criteria, despite providing a basis for solid tumor response evaluation, do not fully encompass this heterogeneity. To better represent these nuances, we introduce the intertumoral heterogeneity response score (THRscore), a measure built upon and expanding the RECIST criteria. This retrospective study included patients with 3-10 measurable advanced lung adenocarcinoma lesions who underwent first-line chemotherapy or targeted therapy. The THRscore, derived from the coefficient of variation in size for each measurable tumor before and 4-6 weeks posttreatment, unveiled a correlation with patient outcomes. Specifically, a high THRscore was associated with shorter progression-free survival, lower tumor response rate, and a higher tumor mutation burden. These associations were further validated in an external cohort, confirming THRscore's effectiveness in stratifying patients based on progression risk and treatment response, and enhancing the utility of RECIST in capturing complex tumor behaviors in lung adenocarcinoma. These findings affirm the promise of THRscore as an enhanced tool for tumor response assessment in advanced lung adenocarcinoma, extending the RECIST criteria's utility.

Modelling-based joint embedding of histology and genomics using canonical correlation analysis for breast cancer survival prediction

Traditional approaches to predicting breast cancer patients' survival outcomes were based on clinical subgroups, the PAM50 genes, or the histological tissue's evaluation. With the growth of multi-modality datasets capturing diverse information (such as genomics, histology, radiology and clinical data) about the same cancer, information can be integrated using advanced tools and have improved survival prediction. These methods implicitly exploit the key observation that different modalities originate from the same cancer source and jointly provide a complete picture of the cancer. In this work, we investigate the benefits of explicitly modelling multi-modality data as originating from the same cancer under a probabilistic framework. Specifically, we consider histology and genomics as two modalities originating from the same breast cancer under a probabilistic graphical model (PGM). We construct maximum likelihood estimates of the PGM parameters based on canonical correlation analysis (CCA) and then infer the underlying properties of the cancer patient, such as survival. Equivalently, we construct CCA-based joint embeddings of the two modalities and input them to a learnable predictor. Real-world properties of sparsity and graph-structures are captured in the penalized variants of CCA (pCCA) and are better suited for cancer applications. For generating richer multi-dimensional embeddings with pCCA, we introduce two novel embedding schemes that encourage orthogonality to generate more informative embeddings. The efficacy of our proposed prediction pipeline is first demonstrated via low prediction errors of the hidden variable and the generation of informative embeddings on simulated data. When applied to breast cancer histology and RNA-sequencing expression data from The Cancer Genome Atlas (TCGA), our model can provide survival predictions with average concordance-indices of up to 68.32% along with interpretability. We also illustrate how the pCCA embeddings can be used for survival analysis through Kaplan-Meier curves.

Leaf Architecture and Genome Size Variation of Durio zibethinus L. from Jelebu, Negeri Sembilan, Malaysia

Durio zibethinus L. is known as the "king of fruit" in Malaysia. Meanwhile, Jelebu, Negeri Sembilan has always become the top choice district to visit for durian lover for its Durian Kampung Jelebu, which possessed good quality on par with top D. zibethinus clones such as D197 Musang King and D24. However, there is still lacking in taxonomic data of D. zibethinus especially from Jelebu. This study aimed to analyse the leaf architecture and genome size variations of selected D. zibethinus accessions from Jelebu. Five D. zibethinus accessions from Jelebu were examined. Thirty-seven parameters of gross leaf morphological characteristics and leaf venation pattern were observed and recorded for identification and classification of D. zibethinus accessions from Jelebu. Seven parameters have been recorded which are petiole length, petiole features, leaf size, leaf shape, leaf base shape, lower leaf surface colour and areolation could be used in differentiating between accessions. Results of this study showed the intraspecific variations existed among D. zibethinus accessions from Jelebu with a genome size varying between 1.7433 pg and 1.800 pg. In conclusion, data on leaf architecture and genome size variations from D. zibethinus accessions are beneficial for early plant identification and classification.

Utilising standard samples instead of randomly collected food waste in composting: Implementation strategy and feasibility evaluation

Randomly collected food waste results in inaccurate experimental data with poor reproducibility for composting. This study investigated standard food waste samples as replacements for randomly collected food waste. A response surface methodology was utilised to analyse data from a 28-day compost process optimisation experiment using collected food waste, and the optimal combination of composting parameters was derived. Experiments using different standard food waste samples (high oil and salt, high oil and sugar, balanced diet, and vegetarian) were conducted for 28 days under optimal conditions. The ranking of differences between the standard samples and collected food waste was vegetarian > balanced diet > high oil and sugar > high oil and salt. Statistical analysis indicated t-tests for increased oil and salt samples and collected food waste were not significant, and Cohen's d effect values were minimal. High oil and salt samples can be used as replacements for collected food waste in composting experiments.

Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation

Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, and ammonium nitrate), followed by nitrogen starvation. Analyses of exudates with liquid chromatography-tandem mass spectrometry, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0's low intratreatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids-peptides and alkaloids. Comparatively, nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p-coumaric acids) on soil bacteria or Brachypodium seedlings revealed their distinct capacity to regulate both bacterial and plant growth. Our results suggest that (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth, and (ii) EcoFAB 2.0 is a valuable standardized plant research tool.

Morphological variability or inter-observer bias? A methodological toolkit to improve data quality of multi-researcher datasets for the analysis of morphological variation

OBJECTIVES

The investigation of morphological variation in animals is widely used in taxonomy, ecology, and evolution. Using large datasets for meta-analyses has dramatically increased, raising concerns about dataset compatibilities and biases introduced by contributions of multiple researchers.

MATERIALS AND METHODS

We compiled morphological data on 13 variables for 3073 individual mouse lemurs (Cheirogaleidae, Microcebus spp.) from 25 taxa and 153 different sampling locations, measured by 48 different researchers. We introduced and applied a filtering pipeline and quantified improvements in data quality (Shapiro-Francia statistic, skewness, and excess kurtosis). The filtered dataset was then used to test for genus-wide sexual size dimorphism and the applicability of Rensch's, Allen's, and Bergmann's rules.

RESULTS

Our pipeline reduced inter-observer bias (i.e., increased normality of data distributions). Inter-observer reliability of measurements was notably variable, highlighting the need to reduce data collection biases. Although subtle, we found a consistent pattern of sexual size dimorphism across Microcebus, with females being the larger (but not heavier) sex. Sexual size dimorphism was isometric, providing no support for Rensch's rule. Variations in tail length but not in ear size were consistent with the predictions of Allen's rule. Body mass and length followed a pattern contrary to predictions of Bergmann's rule.

DISCUSSION

We highlighted the usefulness of large multi-researcher datasets for testing ecological hypotheses after correcting for inter-observer biases. Using genus-wide tests, we outlined generalizable patterns of morphological variability across all mouse lemurs. This new methodological toolkit aims to facilitate future large-scale morphological comparisons for a wide range of taxa and applications.

Morphological and molecular characterization of Stomachicola muraenesocis Yamaguti, 1934 (Digenea: Hemiuridae) from the daggertooth pike conger Muraenesox cinereus (Forsskål)

Hemiurid digeneans conspecific with Stomachicola muraenesocis Yamaguti, 1934 (the type species of the genus Stomachicola Yamaguti, 1934) were collected from the stomach of the daggertooth pike conger Muraenesox cinereus (Forsskål) off the Persian Gulf of Iran. This study aimed to provide a detailed characterization of Stom. muraenesocis, including measurements, illustrations and scanning electron microscopy (s.e.m.) representations. Comparisons with the original and previous descriptions revealed morphological and metrical variations in several features (i.e. body size and shape, arrangement of reproductive organs, soma to ecsoma length ratio, position of genital opening, number of vitelline tubules and extension of uterine coils) between Stom. muraenesocis from different hosts and localities. This study presents the first molecular sequence data associated with the small (18S) and large (28S) subunit nuclear ribosomal RNA genes (rDNA) for Stom. muraenesocis. Phylogenetic analyses of the 18S dataset placed Stom. muraenesocis as sister lineage to a clade formed of a group of species of Lecithaster Lühe, 1901 (Lecithasteridae Odhner, 1905). In contrast, phylogenetic analyses based on the 28S consistently recovered a sister relationship between Stom. muraenesocis and representatives of the Hemiuridae Looss, 1899. Further comprehensive phylogenetically based classification in light of morphology and taxonomic history of the Hemiuridae and Lecithasteridae is required to infer phylogenetic affinities and historical biogeography of Stomachicola. A comprehensive list of previously reported species of Stomachicola together with their associated hosts, localities and morphometric data is provided.

Low interspecific variation and no phylogenetic signal in additive genetic variance in wild bird and mammal populations

Evolutionary adaptation through genetic change requires genetic variation and is a key mechanism enabling species to persist in changing environments. Although a substantial body of work has focused on understanding how and why additive genetic variance (V A) differs among traits within species, we still know little about how they vary among species. Here we make a first attempt at testing for interspecific variation in two complementary measures of V A and the role of phylogeny in shaping this variation. To this end, we performed a phylogenetic comparative analysis using 1822 narrow-sense heritability (h 2) for 68 species of birds and mammals and 378 coefficients of additive genetic variance (CV A) estimates for 23 species. Controlling for within-species variation attributable to estimation method and trait type, we found some interspecific variation in h 2 (~15%) but not CV A. Although suggestive of interspecific variation in the importance of non-(additive) genetic sources of variance, sample sizes were insufficient to test this hypothesis directly. Additionally, although power was low, no phylogenetic signal was detected for either measure. Hence, while this suggests interspecific variation in V A is probably small, our understanding of interspecific variation in the adaptive potential of wild vertebrate populations is currently hampered by data limitations, a scarcity of CV A estimates and a measure of their uncertainty in particular.

Improvement of speed-accuracy tradeoff during practice of a point-to-point task in children with acquired dystonia

The tradeoff between speed and accuracy is a well-known constraint for human movement, but previous work has shown that this tradeoff can be modified by practice, and the quantitative relationship between speed and accuracy may be an indicator of skill in some tasks. We have previously shown that children with dystonia are able to adapt their movement strategy in a ballistic throwing game to compensate for increased variability of movement. Here, we test whether children with dystonia can adapt and improve skills learned on a trajectory task. We use a novel task in which children move a spoon with a marble between two targets. Difficulty is modified by changing the depth of the spoon. Our results show that both healthy children and children with acquired dystonia move more slowly with the more difficult spoons, and both groups improve the relationship between speed and spoon difficulty following 1 wk of practice. By tracking the marble position in the spoon, we show that children with dystonia use a larger fraction of the available variability, whereas healthy children adopt a much safer strategy and remain farther from the margins, as well as learning to adapt and have more control over the marble's utilized area by practice. Together, our results show that both healthy children and children with dystonia choose trajectories that compensate for risk and inherent variability, and that the increased variability in dystonia can be modified with continued practice.NEW & NOTEWORTHY This study provides insights into the adaptability of children with dystonia in learning a point-to-point task. We show that these children adjust their strategies to account for increased difficulty in the task. Our findings underscore the potential of task-specific practice in improving motor skills and show higher level of signal-dependent noise can be controlled through repetition and learned strategies, which provides an avenue for the quantitative evaluation of rehabilitation strategies in this challenging group.

Reliability Associated with the Measurement of Continuous Variables in Veterinary Medicine: What the Different Possible Indicators Tell, and How to Use and Report Them

Reliable indicators of health status (heart rate, rectal temperature, blood marker, etc.) are of cornerstone importance in the daily practice of veterinary medicine. The reliability of a measurement assesses the variability that is associated with the variable to be measured itself vs. other sources of variation (measurement device, person performing the measurement, etc.). Quantitative and continuous indicators are numerous in practice and the determination of their reliability is a complex issue. In the absence of a gold standard approach, several indicators of reliability have been described and can be used depending on several assumptions, study design, and type of measurement. The aim of this manuscript is, therefore, to determine the applicability of commonly described reliability indicators. After a description of the different sources of errors of a measurement, a review of the different indicators that are commonly used in the veterinary field as well as their applicability, limitations, and interpretations is performed.

An environmental habitat gradient and within-habitat segregation enable co-existence of ecologically similar bird species

Niche theory predicts that ecologically similar species can coexist through multidimensional niche partitioning. However, owing to the challenges of accounting for both abiotic and biotic processes in ecological niche modelling, the underlying mechanisms that facilitate coexistence of competing species are poorly understood. In this study, we evaluated potential mechanisms underlying the coexistence of ecologically similar bird species in a biodiversity-rich transboundary montane forest in east-central Africa by computing niche overlap indices along an environmental elevation gradient, diet, forest strata, activity patterns and within-habitat segregation across horizontal space. We found strong support for abiotic environmental habitat niche partitioning, with 55% of species pairs having separate elevation niches. For the remaining species pairs that exhibited similar elevation niches, we found that within-habitat segregation across horizontal space and to a lesser extent vertical forest strata provided the most likely mechanisms of species coexistence. Coexistence of ecologically similar species within a highly diverse montane forest was determined primarily by abiotic factors (e.g. environmental elevation gradient) that characterize the Grinnellian niche and secondarily by biotic factors (e.g. vertical and horizontal segregation within habitats) that describe the Eltonian niche. Thus, partitioning across multiple levels of spatial organization is a key mechanism of coexistence in diverse communities.

Response Characteristics Study of Ethylene Sensor for Fruit Ripening under Temperature Control

Post-ripening fruits need to be ripened to reach edible conditions, as they are not yet mature enough when picked. Ripening technology is based mainly on temperature control and gas regulation, with the proportion of ethylene being one of the key gas regulation parameters. A sensor's time domain response characteristic curve was obtained through the ethylene monitoring system. The first experiment showed that the sensor has good response speed (maximum of first derivative: 2.01714; minimum of first derivative: -2.01714), stability (xg: 2.42%; trec: 2.05%; Dres: 3.28%), and repeatability (xg: 20.6; trec: 52.4; Dres: 2.31). The second experiment showed that optimal ripening parameters include color, hardness (Change Ⅰ: 88.53%, Change Ⅱ: 75.28%), adhesiveness (Change Ⅰ: 95.29%, Change Ⅱ: 74.72%), and chewiness (Change Ⅰ: 95.18%, Change Ⅱ: 74.25%), verifying the response characteristics of the sensor. This paper proves that the sensor was able to accurately monitor changes in concentration which reflect changes in fruit ripeness, and that the optimal parameters were the ethylene response parameter (Change Ⅰ: 27.78%, Change Ⅱ: 32.53%) and the first derivative parameter (Change Ⅰ: 202.38%, Change Ⅱ: -293.28%). Developing a gas-sensing technology suitable for fruit ripening is of great significance.

Improvement of speed-accuracy tradeoff during practice of a point to point task in children with secondary dystonia

The tradeoff between speed and accuracy is a well-known constraint for human movement, but previous work has shown that this tradeoff can be modified by practice, and the quantitative relationship between speed and accuracy may be an indicator of skill in some tasks. We have previously shown that children with dystonia are able to adapt their movement strategy in a ballistic throwing game to compensate for increased variability of movement. Here we test whether children with dystonia can adapt and improve skill learnt on a trajectory task. We use a novel task in which children move a spoon with a marble between two targets. Difficulty is modified by changing the depth of the spoon. Our results show that both healthy children and children with secondary dystonia move more slowly with the more difficult spoons, and both groups improve the relationship between speed and spoon difficulty following one week of practice. By tracking the marble position in the spoon, we show that children with dystonia use a larger fraction of the available variability, whereas healthy children adopt a much safer strategy and remain farther from the margins, as well as learning to adopt and have more control over the marble's utilized area by practice. Together, our results show that both healthy children and children with dystonia choose trajectories that compensate for risk and inherent variability, and that the increased variability in dystonia can be modified with continued practice.

Quartile coefficient of variation is more robust than CV for traits calculated as a ratio

Comparing within-species variations of traits can be used in testing ecological theories. In these comparisons, it is useful to remove the effect of the difference in mean trait values, therefore measures of relative variation, most often the coefficient of variation (CV), are used. The studied traits are often calculated as the ratio of the size or mass of two organs: e.g. specific leaf area (SLA) is the ratio of leaf size and leaf mass. Often the inverse of these ratios is also meaningful; for example, the inverse of SLA is often referred to as LMA (leaf mass per area). Relative variation of a trait and its inverse should not considerably differ. However, it is illustrated that using the coefficient of variation may result in differences that could influence the interpretation, especially if there are outlier trait values. The alternative way for estimating CV from the standard deviation of log-transformed data assuming log-normal distribution and Kirkwood's geometric coefficient of variation free from this problem, but they proved to be sensitive to outlier values. Quartile coefficient of variation performed best in the tests: it gives the same value for a trait and its inverse and it is not sensitive to outliers.

Carbon Nanotube-Incorporated Nanofibers for Immunosensor Preparation against CD36

The increased serum concentration of CD36 is significantly associated with atherosclerosis, insulin resistance, and diabetes mellitus. Currently, there is no sensor system used for the detection of CD36 in the clinical field. Therefore, there is a need to develop a sensor system for the detection of CD36. The large surface area/volume ratio and controllable surface conformation of electrospun nanofibers (ENs) make them highly attractive for immunosensor applications. In the present study, PS/MWCNT-PAMAM ENs were produced and used as an immobilization matrix of Anti-CD36. Thus, the electrochemical behavior of the developed nanocomposite-based ENs and their usage potential were investigated for immunosensor applications. First, an oxidized multiwall carbon nanotube (MWCNT-OH) was synthesized and modified with a polyamidoamine generation 3 (PAMAM G3) dendrimer. The synthesized MWCNT-PAMAM nanocomposite was mixed with polystyrene (PS) solutions at different ratios to produce bead-free, smooth, and uniform PS/MWCNT-PAMAM ENs. PS/MWCNT-PAMAM ENs were accumulated on a screen-printed carbon electrode (SPCE) using the electrospinning technique. A biofunctional surface on the PS/MWCNT-PAMAM EN-coated SPCE was created using carbodiimide chemistry by covalent immobilization of Anti-CD36. The analytic performance characteristics of the developed PS/MWCNT-PAMAM/Anti-CD36 immunosensor were determined by performing electrochemical measurements in the presence of the CD36 protein. The linear detection range was found to be from 5 to 40 ng/mL, and the limit of detection was calculated as 3.94 ng/mL for CD36. The developed PS/MWCNT-PAMAM/Anti-CD36 immunosensor also displayed high tolerance to interference substances, good repeatability, and high recovery percent (recovery%) for artificial blood serum analysis.

Progress in Discovering Transcriptional Noise in Aging

Increasing stochasticity is a key feature in the aging process. At the molecular level, in addition to genome instability, a well-recognized hallmark of aging, cell-to-cell variation in gene expression was first identified in mouse hearts. With the technological breakthrough in single-cell RNA sequencing, most studies performed in recent years have demonstrated a positive correlation between cell-to-cell variation and age in human pancreatic cells, as well as mouse lymphocytes, lung cells, and muscle stem cells during senescence in vitro. This phenomenon is known as the "transcriptional noise" of aging. In addition to the increasing evidence in experimental observations, progress also has been made to better define transcriptional noise. Traditionally, transcriptional noise is measured using simple statistical measurements, such as the coefficient of variation, Fano factor, and correlation coefficient. Recently, multiple novel methods have been proposed, e.g., global coordination level analysis, to define transcriptional noise based on network analysis of gene-to-gene coordination. However, remaining challenges include a limited number of wet-lab observations, technical noise in single-cell RNA sequencing, and the lack of a standard and/or optimal data analytical measurement of transcriptional noise. Here, we review the recent technological progress, current knowledge, and challenges to better understand transcriptional noise in aging.

Spatially and temporally varying selection influence species boundaries in two sympatric Mimulus

Spatially and temporally varying selection can maintain genetic variation within and between populations, but it is less well known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely related Mimulus species. Using repeated reciprocal transplant experiments with advanced generation hybrids, we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation in Mimulus guttatus and Mimulus laciniatus between two years with dramatically different water availability. We found strong divergent habitat-mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time, which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence.

Do mean values tell the full story? Cardiac cycle and biological sex comparisons in temporally derived neurovascular coupling metrics

Previous reports have noted cerebrovascular regulation differs across the cardiac cycle, with greater regulation occurring within systole. However, this methodological notion has not been meticulously scrutinized during temporally deduced neurovascular coupling (NVC) metrics with additional respect to biological sex. Analyses of 111 healthy individuals (40 females/71 males) were performed where participants engaged in the "Where's Waldo?" paradigm. All NVC parameters were quantified in the posterior and middle cerebral arteries at 310 unique timepoints. Several individuals completed repeat testing which enabled for between-day (3 timepoints) and within-day (7 timepoints) reliability comparisons in 17 and 11 individuals, respectively. One-way analysis of variance compared NVC metrics between diastole, mean, and systole values, as well as differences between biological sexes. Greater absolute cerebral blood velocity (CBv; baseline and peak) and total activation (area under the curve) were noted within systole for both posterior cerebral artery (PCA; P < 0.001) and middle cerebral artery (MCA; P < 0.001) values; however, the relative percent increase in CBv was greater within diastole (P < 0.001). Females had an elevated diastolic and mean CBv and a greater diastolic cerebrovascular conductance (P < 0.050). No sex differences were present for systolic CBv measures and within parameters quantifying the NVC response (area under the curve/relative CBv increase) across the cardiac cycle (P > 0.072). Future investigations seeking to differentiate cerebral regulatory mechanisms between clinical populations may benefit by performing their analyses across the cardiac cycle, as certain pathogenesis may affect one aspect of the cardiac cycle independently. Minimal differences were noted between females and males for metrics characterizing the NVC response across the cardiac cycle.NEW & NOTEWORTHY Neurovascular coupling (NVC) studies commonly assess the mean cerebral hemodynamic response with little consideration for diastole, systole, and biological sex. Greater total activation expressed as the area under the curve was seen within systole compared with mean and diastole. Resting cerebral blood velocity sex differences were more prevalent during diastole when the cerebrovasculature was pressure-passive. Future studies should assess the NVC response across the cardiac cycle as it may help delineate the underlying pathophysiology of various clinical populations.

Evaluation and Impact Mechanism of High-Quality Development in China's Coastal Provinces

With economic expansion having moderated to a "new normal" pace, the eastern coastal provinces have been given a new historical task of high-quality development and become a window and frontier of China's high-quality development. By designing and optimizing an index system of high-quality development levels and using the entropy-TOPSIS method, the study selected 21 indicators, include economic vitality, residents' living standards, innovation efficiency and green development, and took China's eastern coastal provinces as an example to study the characteristics of spatial-temporal variations in the high-quality development level from 2010 to 2020. Then, the study used the obstacle degree model to explore the factors that are obstacles to high-quality development. The results show that the high-quality development of the eastern coastal provinces presents an "up-down-up" fluctuation, with an increase of 40.1%. In particular, the development level of the residents' living standards dimension is higher, and the high-quality development level of each province shows different degrees of growth and gradually tends to balanced development, with the high-quality development of Shanghai, Jiangsu Province and Zhejiang Province in a dominant position. The spatial pattern of high-quality development in the study areas shows a spatial distribution pattern of "high in the east and low in the west, high in the north and low in the south", in which the bipolar spatial effect of the innovation efficiency dimension is becoming more and more prominent, while the regional synergistic development effect of the residents' living standard dimension is more obvious, and the high-quality development spatial pattern shows a "core-periphery" structure, and there is a path-dependent effect in time change, and agglomeration is produced by trickle-down effect in space. The obstacles to residents' living standards are high, and the main obstacle factor has gradually changed from insufficient output in innovation to a reduction in the scale of foreign trade. In addition, the problems of unreasonable industrial structure and shortage of per capita public cultural resources still exist. In provinces with a high-quality development level and a relatively developed economy, the biggest obstacle factors are economic vitality and residents' living standards. In provinces with a low level of high-quality development and a relatively backward economy, the biggest obstacle factors are green development and innovation efficiency, and there are both similarities and differences in the main obstacle factors among provinces.

Root System Traits Contribute to Variability and Plasticity in Response to Phosphorus Fertilization in 2 Field-Grown Sorghum [Sorghum bicolor (L.) Moench] Cultivars

Due to roots' physical and physiological roles in crop productivity, interest in root system architecture (RSA) and plasticity in responses to abiotic stresses is growing. Sorghum is significant for the food security of millions of people. Phosphorus deficiency is an important limitation of sorghum productivity. There is little information on the RSA-based responses of sorghum to variations in external P supply ([P]_ext). This study evaluated the phenotypic plasticity and RSA responses to a range of [P]_ext in 2 sorghum genotypes. The results showed that both genotypes responded to [P]_ext but with significant variations in about 80% of the RSA traits analyzed. Aboveground biomass and most RSA traits increased with increasing [P]_ext. Plasticity was both genotype- and trait-dependent. For most RSA traits, the white sorghum genotype showed significantly higher plasticity than the red genotype, with the former having about 28.4% higher total plasticity than the former. RSA traits, such as convex area, surface area, total root length, and length diameter ranges, showed sizeable genetic variability. Root biomass had a high degree of plasticity, but root number and angle traits were the leading contributors to variation. The results suggested 2 root trait spectra: root exploration and developmental spectrum, and there was an indication of potential trade-offs among groups of root traits. It is concluded that RSA traits in sorghum contribute to variability and plasticity in response to [P]_ext. Given that there might be trade-offs among sorghum root traits, it would be instructive to determine the fundamental constraints underlying these trade-offs.

Characterization, costs, cues and future perspectives of phenotypic plasticity

BACKGROUND

Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness and the environmental cues that regulate its expression.

SCOPE

This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret and respond to environmental cues, and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs and limits to expression of plasticity. The timing, specificity and duration of plasticity are critical to their adaptive value for plant fitness.

CONCLUSIONS

There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding the mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.

Neurovascular coupling on trial: How the number of trials completed impacts the accuracy and precision of temporally derived neurovascular coupling estimates

Standard practices for quantifying neurovascular coupling (NVC) with transcranial Doppler ultrasound (TCD) require participants to complete one-to-ten repetitive trials. However, limited empirical evidence exists regarding how the number of trials completed influences the validity and reliability of temporally derived NVC metrics. Secondary analyses was performed on 60 young healthy participants (30 females/30 males) who completed eight cyclical eyes-closed (20-seconds), eyes-open (40-seconds) NVC trials, using the "Where's Waldo?" visual paradigm. TCD data was obtained in posterior and middle cerebral arteries (PCA and MCA, respectively). The within-day (n = 11) and between-day (n = 17) reliability were assessed at seven- and three-time points, respectively. Repeat testing from the reliability aims were also used for the concurrent validity analysis (n = 160). PCA metrics (i.e., baseline, peak, percent increase, and area-under-the-curve) demonstrated five trials produced excellent intraclass correlation coefficient (ICC) 95% confidence intervals for validity and within-day reliability (>0.900), whereas between-day reliability was good-to-excellent (>0.750). Likewise, 95% confidence intervals for coefficient of variation (CoV) measures ranged from acceptable (<20%) to excellent (<5%) with five-or-more trials. Employing fewer than five trials produced poor/unacceptable ICC and CoV metrics. Future NVC, TCD-based research should therefore have participants complete a minimum of five trials when quantifying the NVC response with TCD via a "Where's Waldo?" paradigm.

Polyploidization: Consequences of genome doubling on the evolutionary potential of populations

Whole-genome duplication is common in plants and is considered to have a broad range of effects on individuals' phenotypes and genomes and to be an important driver of plant adaptation and speciation. Despite their increased capacity to cope with challenging environments, polyploid lineages are generally as prone to extinction, and sometimes more prone, than their diploid progenitors. Although several explanations have been proposed to explain the short- and long-term disadvantages of polyploidy on the survival probability of populations, the consequences of whole-genome doubling on the heritable variance remain poorly studied. Whole-genome doubling can have major effects not only on the genetics, but also on the ecology and life history of the populations. Modifications of other properties of populations can reverse the effects of polyploidization per se on heritable variance. In this synthesis, I summarize the empirical and theoretical knowledge about the multifarious consequences of genome doubling on the heritable variance of quantitative traits and on the evolutionary potential of polyploid populations compared to their diploid progenitors. I propose several ways to decipher the consequences of whole-genome doubling on survival probability and to study the further consequences of shifting the ecological niche and life-history traits of a population. I also highlight some practical considerations for comparing the heritable variance of a trait among different cytotypes. Such investigations appear to be timely and necessary to understand more about the paradoxical aspects of polyploidization and to understand the evolutionary potential of polyploid lineages in a global warming context.

Bayesian Inference-Based Gaussian Mixture Models With Optimal Components Estimation Towards Large-Scale Synthetic Data Generation for In Silico Clinical Trials

Goal: To develop a computationally efficient and unbiased synthetic data generator for large-scale in silico clinical trials (CTs). Methods: We propose the BGMM-OCE, an extension of the conventional BGMM (Bayesian Gaussian Mixture Models) algorithm to provide unbiased estimations regarding the optimal number of Gaussian components and yield high-quality, large-scale synthetic data at reduced computational complexity. Spectral clustering with efficient eigenvalue decomposition is applied to estimate the hyperparameters of the generator. A case study is conducted to compare the performance of BGMM-OCE against four straightforward synthetic data generators for in silico CTs in hypertrophic cardiomyopathy (HCM). Results: The BGMM-OCE generated 30000 virtual patient profiles having the lowest coefficient-of-variation (0.046), inter- and intra-correlation differences (0.017, and 0.016, respectively) with the real ones in reduced execution time. Conclusions: BGMM-OCE overcomes the lack of population size in HCM which obscures the development of targeted therapies and robust risk stratification models.

Inter- and intra-scan variability for lung imaging quantifications via CT

CT imaging provides physicians valuable insights when diagnosing disease in a clinical setting. In order to provide an accurate diagnosis, is it important to have a high accuracy with controlled variability across CT scans from different scanners and imaging parameters. The purpose of this study was to analyze variability of lung imaging biomarkers across various scanners and parameters using a customized version of a commercially available anthropomorphic chest Phantom (Kyoto Kagaku) with several experimental sample inserts. The phantom was across 10 different CT scanners with a total of 209 imaging conditions. An algorithm was developed to compute different imaging biomarkers. Variability across images from the same scanner and from different scanners was analyzed by computing coefficients of variation (CV) and standard deviations of HU values. LAA -950 and LAA -856 biomarkers had the highest levels of variability, while the majority of other biomarkers had variability less than 10 HU or 10% CV in both inter and intra-scan measurements. There was no clear trend present between the biomarker measurements and CTDIvol. The results of this study demonstrates the existing variability in CT quantifications for lung imaging, which prompt further studies on how to reduce such variation.

Delaying effect of humidity on leaf unfolding in Europe

Understanding the drivers of plant phenology is critical to predict the impact of future warming on terrestrial ecosystem carbon cycling and feedbacks to climate. Using indoor growth chambers, air humidity is reported to influence spring phenology in temperate trees. However, previous studies have not investigated the effect of air humidity on the spring phenology using long-term and large-scale ground observations. Therefore, the role of humidity in spring phenology in temperate trees still remains poorly understood. Here, we synthesized 229,588 records of leaf unfolding dates in eight temperate tree species, including four early-successional and four late-successional species, at 1716 observation sites during 1951-2015 in Europe, and comprehensively analyzed the effect of humidity on the spring phenology. We found that rising humidity significantly delayed spring leaf unfolding for all eight temperate tree species. Leaf unfolding was more sensitive to humidity in early-successional species compared to late-successional species. In addition, the delaying effect of humidity on leaf unfolding increased as temperature warmed over the past 65 years. Our results provide evidence that spring leaf unfolding of temperate trees was significantly delayed by rising humidity. The delaying effect of humidity may restrict earlier spring phenology induced by warming, especially for early-successional species, under future climate warming scenarios in temperate forests.

Public transcriptome database-based selection and validation of reliable reference genes for breast cancer research

BACKGROUND

Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes (RGs) is critical for normalizing and evaluating changes in the expression of target genes. However, uniform and reliable RGs for breast cancer research have not been identified, limiting the value of target gene expression studies. Here, we aimed to identify reliable and accurate RGs for breast cancer tissues and cell lines using the RNA-seq dataset.

METHODS

First, we compiled the transcriptome profiling data from the TCGA database involving 1217 samples to identify novel RGs. Next, ten genes with relatively stable expression levels were chosen as novel candidate RGs, together with six conventional RGs. To determine and validate the optimal RGs we performed qRT-PCR experiments on 87 samples from 11 types of surgically excised breast tumor specimens (n = 66) and seven breast cancer cell lines (n = 21). Five publicly available algorithms (geNorm, NormFinder, ΔCt method, BestKeeper, and ComprFinder) were used to assess the expression stability of each RG across all breast cancer tissues and cell lines.

RESULTS

Our results show that RG combinations SF1 + TRA2B + THRAP3 and THRAP3 + RHOA + QRICH1 showed stable expression in breast cancer tissues and cell lines, respectively, and that they displayed good interchangeability. We propose that these combinations are optimal triplet RGs for breast cancer research.

CONCLUSIONS

In summary, we identified novel and reliable RG combinations for breast cancer research based on a public RNA-seq dataset. Our results lay a solid foundation for the accurate normalization of qRT-PCR results across different breast cancer tissues and cells.